NIfTI: Difference between revisions
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Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI medical image format]; it is becoming a standard export format for many different software packages, including [http://www.fmrib.ox.ac.uk/fsl/ FSL]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library. | Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI medical image format]; it is becoming a standard export format for many different software packages, including [http://www.fmrib.ox.ac.uk/fsl/ FSL]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library. | ||
=Paths= | == Paths == | ||
<code>$G/src/nifti</code> is the source code for the NIfTI I/O library, which installs to <code>$G/lib/nifti</code> and <code>$G/include/nifti</code>. | <code>$G/src/nifti</code> is the source code for the NIfTI I/O library, which installs to <code>$G/lib/nifti</code> and <code>$G/include/nifti</code>. | ||
=Use= | == Use == | ||
=== Library === | |||
To use the NIfTI I/O library, simply <code>#include <nifti1_io.h></code> in your code and add the following to the library list in your makefile: <code>niftiio znz m z</code>. | To use the NIfTI I/O library, simply <code>#include <nifti1_io.h></code> in your code and add the following to the library list in your makefile: <code>niftiio znz m z</code>. | ||
<code>$G/src/nifti2mriimage/nifti2mriimage.cpp</code> demonstrates reading the header and extracting information from it, as well as reading the image data. | <code>$G/src/nifti2mriimage/nifti2mriimage.cpp</code> demonstrates reading the header and extracting information from it, as well as reading the image data. | ||
=== Command-Line Utilities === | |||
The <code>nifti_tool</code> utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it. | |||
=Documentation= | === Format Conversion === | ||
<code>$G/bin/nifti2mriimage</code> converts to MRIimage. | |||
== Documentation == | |||
<code>make install</code> puts some documentation in <code>$G/doc/nifti</code>. However, the online documentation for NIfTI is probably even better and more useful: | <code>make install</code> puts some documentation in <code>$G/doc/nifti</code>. However, the online documentation for NIfTI is probably even better and more useful: | ||
* [http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/ NIfTI-1 Header Field Description] | * [http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/ NIfTI-1 Header Field Description] | ||
* [http://nifti.nimh.nih.gov/nifti-1/documentation/faq NIfTI FAQ] | * [http://nifti.nimh.nih.gov/nifti-1/documentation/faq NIfTI FAQ] | ||
=History= | == History == | ||
The format was created by the [http://nifti.nimh.nih.gov Neuroimaging Informatics Technology Initiative] at NIH. It is a superset of Analyze 7.5, re-purposing empty fields in the Analyze format to support more features. Fortunately for us, the NIfTI reference library is available in the public domain, and <code>$G/src/nifti</code> is set up to download the latest version (with <code>make download</code>), build it, and install it. NIfTI is an actively developed format, but the NIfTI-1 specification is fixed; NIfTI-2 will be formulated and released at some point in the future. | The format was created by the [http://nifti.nimh.nih.gov Neuroimaging Informatics Technology Initiative] at NIH. It is a superset of Analyze 7.5, re-purposing empty fields in the Analyze format to support more features. Fortunately for us, the NIfTI reference library is available in the public domain, and <code>$G/src/nifti</code> is set up to download the latest version (with <code>make download</code>), build it, and install it. NIfTI is an actively developed format, but the NIfTI-1 specification is fixed; NIfTI-2 will be formulated and released at some point in the future. | ||
Revision as of 20:56, 21 August 2008
Files ending in .nii are in the NIfTI medical image format; it is becoming a standard export format for many different software packages, including FSL. .nii files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in .hdr/.img pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension .nii.gz. You can test for the format by using the is_nifti_file() function in the I/O library.
Paths
$G/src/nifti is the source code for the NIfTI I/O library, which installs to $G/lib/nifti and $G/include/nifti.
Use
Library
To use the NIfTI I/O library, simply #include <nifti1_io.h> in your code and add the following to the library list in your makefile: niftiio znz m z.
$G/src/nifti2mriimage/nifti2mriimage.cpp demonstrates reading the header and extracting information from it, as well as reading the image data.
Command-Line Utilities
The nifti_tool utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it.
Format Conversion
$G/bin/nifti2mriimage converts to MRIimage.
Documentation
make install puts some documentation in $G/doc/nifti. However, the online documentation for NIfTI is probably even better and more useful:
History
The format was created by the Neuroimaging Informatics Technology Initiative at NIH. It is a superset of Analyze 7.5, re-purposing empty fields in the Analyze format to support more features. Fortunately for us, the NIfTI reference library is available in the public domain, and $G/src/nifti is set up to download the latest version (with make download), build it, and install it. NIfTI is an actively developed format, but the NIfTI-1 specification is fixed; NIfTI-2 will be formulated and released at some point in the future.